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I'm not sure what this actually entails. Should features be disabled if an "old" version of the database is specified? That seems pretty complicated, let alone trying to have totally different behavior of the same feature if a specific database schema version is specified. I vote to push this to at least 1.0, and generally, to try our best to avoid backwards-incompatible changes to the database schema.
I'm not quite sure either. I believe we were thinking more along the lines of specifying the ChemKED (CK? CKED?) format used when creating the file, so that the PyKED could check it and gracefully handle any breaking changes. That does seem like it would be complicated, though.
I agree that this can be pushed off to 1.0. Ideally, we should be able to only add new features, rather than change or delete things, starting at that point.
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